Getting R software¶
Getting R in the first place¶
There are three options for accessing R at Carc and I will run through both approaches since there are pros and cons to each.
Option 1¶
The first option is to activate an installed R module. When logged in to a CARC system you can use the module avail command to see which R versions are available. If you have a CARC account open a terminal and log in to follow along.
which will print out the following (although I have truncated the output):
----------------------- /opt/spack/share/spack/modules/linux-centos7-x86_64 ------------------------
...
r-3.4.1-gcc-4.8.5-python2-gzeg24m
r-3.4.1-gcc-4.8.5-python2-zpkgqap
r-3.4.1-intel-17.0.4-mkl-python2-67zsm3b
r-3.4.1-intel-17.0.4-mkl-python2-gygkoab
r-3.4.2-intel-18.0.2-python2-xsxuxwx
r-3.4.3-gcc-4.8.5-python2-gk66fni
r-3.4.3-gcc-4.8.5-python2-qv6gwz6
r-3.4.3-gcc-6.1.0-python2-lyqiytq
r-3.4.3-gcc-7.3.0-python2-zhxbajj
r-3.4.3-intel-18.0.1-python2-3l4dkgz
r-3.4.3-intel-18.0.1-python2-lr24ix6
r-3.4.3-intel-18.0.2-python2-q3covk7
r-3.5.0-gcc-4.8.5-python2-khqxja7
r-3.5.0-gcc-7.3.0-python2-rvq3qk5
r-3.5.0-intel-18.0.2-python2-mkl-r6lx6yy
r-3.5.3-gcc-7.3.0-python2-ziiolp5
r-3.6.0-gcc-4.8.5-python2-i4uimtp
r-3.6.0-gcc-7.3.0-python2-7akol5t
...
Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
These are the R modules available on the cluster. In order to activate a R software module you use the module load command. For example:
yourusername@hopper$ module load r-3.6.0-gcc-7.3.0-python2-7akol5t
yourusername@hopper$ R
R version 3.6.0 (2019-04-26) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
Will load R-3.6.0 that has been compiled with GCC-7.3.0. Normally you will be running R jobs in batch mode as oppposed to interactively, which means you will have the module load command in your PBS script, but we will get to that later.
Option 2¶
The second option is to create a custom local Anaconda environment with the version of R that would like to run. In order to do this you need to first load an Anaconda software module and then create a new environment according to your specifications. For example, the following commands will create an Anaconda environment with R-3.4.3:
yourusername@hopper$ module load anaconda3
yourusername@hopper$ conda create --yes --name my_r_env r=3.4.3
Solving environment: done
## Package Plan ##
environment location: /users/yourusername/.conda/envs/my_r_env
added / updated specs:
- r=3.4.3
The following packages will be downloaded:
package | build
---------------------------|-----------------
gfortran_linux-64-7.3.0 | h553295d_8 148 KB
r-cluster-2.0.6 | r343h4829c52_0 519 KB
r-lattice-0.20_35 | r343h086d26f_0 713 KB
r-base-3.4.3 | h9bb98a2_5 38.3 MB
r-recommended-3.4.3 | r343_0 3 KB
r-3.4.3 | r343_0 3 KB
r-mgcv-1.8_22 | r343h086d26f_0 2.4 MB
r-matrix-1.2_12 | r343h086d26f_0 2.5 MB
r-kernsmooth-2.23_15 | r343h4829c52_4 101 KB
r-class-7.3_14 | r343h086d26f_4 93 KB
r-nlme-3.1_131 | r343h4829c52_0 2.2 MB
r-foreign-0.8_69 | r343h086d26f_0 256 KB
r-survival-2.41_3 | r343h086d26f_0 5.1 MB
gcc_linux-64-7.3.0 | h553295d_8 149 KB
r-spatial-7.3_11 | r343h086d26f_4 140 KB
gcc_impl_linux-64-7.3.0 | habb00fd_1 73.2 MB
gxx_impl_linux-64-7.3.0 | hdf63c60_1 18.7 MB
gxx_linux-64-7.3.0 | h553295d_8 148 KB
r-boot-1.3_20 | r343h889e2dd_0 625 KB
binutils_linux-64-2.31.1 | h6176602_8 148 KB
r-mass-7.3_48 | r343h086d26f_0 1.1 MB
bzip2-1.0.8 | h7b6447c_0 105 KB
ca-certificates-2019.5.15 | 1 134 KB
r-codetools-0.2_15 | r343h889e2dd_0 49 KB
r-rpart-4.1_11 | r343h086d26f_0 899 KB
r-nnet-7.3_12 | r343h086d26f_0 118 KB
libxml2-2.9.9 | hea5a465_1 2.0 MB
------------------------------------------------------------
Total: 149.8 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex: 0.1-main
_r-mutex: 1.0.0-anacondar_1
binutils_impl_linux-64: 2.31.1-h6176602_1
binutils_linux-64: 2.31.1-h6176602_8
bwidget: 1.9.11-1
bzip2: 1.0.8-h7b6447c_0
ca-certificates: 2019.5.15-1
cairo: 1.14.12-h8948797_3
curl: 7.65.2-hbc83047_0
fontconfig: 2.13.0-h9420a91_0
freetype: 2.9.1-h8a8886c_1
fribidi: 1.0.5-h7b6447c_0
gcc_impl_linux-64: 7.3.0-habb00fd_1
gcc_linux-64: 7.3.0-h553295d_8
gfortran_impl_linux-64: 7.3.0-hdf63c60_1
gfortran_linux-64: 7.3.0-h553295d_8
glib: 2.56.2-hd408876_0
graphite2: 1.3.13-h23475e2_0
gxx_impl_linux-64: 7.3.0-hdf63c60_1
gxx_linux-64: 7.3.0-h553295d_8
harfbuzz: 1.8.8-hffaf4a1_0
icu: 58.2-h9c2bf20_1
jpeg: 9b-h024ee3a_2
krb5: 1.16.1-h173b8e3_7
libcurl: 7.65.2-h20c2e04_0
libedit: 3.1.20181209-hc058e9b_0
libffi: 3.2.1-hd88cf55_4
libgcc-ng: 9.1.0-hdf63c60_0
libgfortran-ng: 7.3.0-hdf63c60_0
libpng: 1.6.37-hbc83047_0
libssh2: 1.8.2-h1ba5d50_0
libstdcxx-ng: 9.1.0-hdf63c60_0
libtiff: 4.0.10-h2733197_2
libuuid: 1.0.3-h1bed415_2
libxcb: 1.13-h1bed415_1
libxml2: 2.9.9-hea5a465_1
ncurses: 6.1-he6710b0_1
openssl: 1.1.1c-h7b6447c_1
pango: 1.42.4-h049681c_0
pcre: 8.43-he6710b0_0
pixman: 0.38.0-h7b6447c_0
r: 3.4.3-r343_0
r-base: 3.4.3-h9bb98a2_5
r-boot: 1.3_20-r343h889e2dd_0
r-class: 7.3_14-r343h086d26f_4
r-cluster: 2.0.6-r343h4829c52_0
r-codetools: 0.2_15-r343h889e2dd_0
r-foreign: 0.8_69-r343h086d26f_0
r-kernsmooth: 2.23_15-r343h4829c52_4
r-lattice: 0.20_35-r343h086d26f_0
r-mass: 7.3_48-r343h086d26f_0
r-matrix: 1.2_12-r343h086d26f_0
r-mgcv: 1.8_22-r343h086d26f_0
r-nlme: 3.1_131-r343h4829c52_0
r-nnet: 7.3_12-r343h086d26f_0
r-recommended: 3.4.3-r343_0
r-rpart: 4.1_11-r343h086d26f_0
r-spatial: 7.3_11-r343h086d26f_4
r-survival: 2.41_3-r343h086d26f_0
readline: 7.0-h7b6447c_5
tk: 8.6.8-hbc83047_0
tktable: 2.10-h14c3975_0
xz: 5.2.4-h14c3975_4
zlib: 1.2.11-h7b6447c_3
zstd: 1.3.7-h0b5b093_0
Downloading and Extracting Packages
gfortran_linux-64-7. | 148 KB | ########################################################### | 100%
r-cluster-2.0.6 | 519 KB | ########################################################### | 100%
r-lattice-0.20_35 | 713 KB | ########################################################### | 100%
r-base-3.4.3 | 38.3 MB | ########################################################### | 100%
r-recommended-3.4.3 | 3 KB | ########################################################### | 100%
r-3.4.3 | 3 KB | ########################################################### | 100%
r-mgcv-1.8_22 | 2.4 MB | ########################################################### | 100%
r-matrix-1.2_12 | 2.5 MB | ########################################################### | 100%
r-kernsmooth-2.23_15 | 101 KB | ########################################################### | 100%
r-class-7.3_14 | 93 KB | ########################################################### | 100%
r-nlme-3.1_131 | 2.2 MB | ########################################################### | 100%
r-foreign-0.8_69 | 256 KB | ########################################################### | 100%
r-survival-2.41_3 | 5.1 MB | ########################################################### | 100%
gcc_linux-64-7.3.0 | 149 KB | ########################################################### | 100%
r-spatial-7.3_11 | 140 KB | ########################################################### | 100%
gcc_impl_linux-64-7. | 73.2 MB | ########################################################### | 100%
gxx_impl_linux-64-7. | 18.7 MB | ########################################################### | 100%
gxx_linux-64-7.3.0 | 148 KB | ########################################################### | 100%
r-boot-1.3_20 | 625 KB | ########################################################### | 100%
binutils_linux-64-2. | 148 KB | ########################################################### | 100%
r-mass-7.3_48 | 1.1 MB | ########################################################### | 100%
bzip2-1.0.8 | 105 KB | ########################################################### | 100%
ca-certificates-2019 | 134 KB | ########################################################### | 100%
r-codetools-0.2_15 | 49 KB | ########################################################### | 100%
r-rpart-4.1_11 | 899 KB | ########################################################### | 100%
r-nnet-7.3_12 | 118 KB | ########################################################### | 100%
libxml2-2.9.9 | 2.0 MB | ########################################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use:
# > source activate my_r_env
#
# To deactivate an active environment, use:
# > source deactivate
#
yourusername@hopper$ module load anaconda3
yourusername@hopper$ source activate my_r_env
yourusername@hopper$ R
R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
Option 3¶
The third option is to user JupyterHub. To do so direct your browser to https://hopper.alliance.unm.edu and log in with your CARC credentials. Click on the "New" drop down menu and select "R". Now you have a R session running on the cluster through JupyterHub.
Migrated from UNM-CARC QuickBytes (last source update 2019-12-11). Spotted a problem? Open an issue or pull request.